return to Lynch Lab main page

Hongan Long
Postdoctoral Researcher

Ph.D., 2012, Biology, University of Houston

M.S., 2007, Marine Biology, Ocean University of China

B.S., 2004, Bioscience, Ocean University of China

Mutation is the ultimate source of genetic variation. However, mutations are notoriously hard to catch, because of their rarity and easy loss due to purifying selection. Mutation accumulation procedures concur these difficulties by setting up large number of replicate cell lines from a single cell ancestor and single-cell/colony transfers on rich media to maximize genetic drift. Most studies on spontaneous mutations were based on indirect methods to derive mutation rates, for example, synonymous site or pseudogene mutation rate through DNA sequence comparison between different organisms, reporter construct based on only one or a handful genes, or fitness assays on mutation accumulation lines. Since 2008, when whole-genome sequencing began to be commercially available, the Lynch lab started directly detecting mutations by deeply sequencing the mutation accumulation lines.

My post-doc research focuses on:

  1. Explore mutation rates and spectra of unicellular microbes, including bacteria and eukaryotes, broadly sampled from the Tree of Life, as well as factors influencing mutation rates. Up to date, the findings are: mutations are not random, mutation rate of a single nucleotide is influenced by the flanking nucleotide and the genomic position; there are exceptions of the “universal A/T bias” of bacteria, and mutation types of an organism could be highly variable and influenced by the biology and the outside environment, though mutation rate per genome per generation does not vary much; unicellular eukaryotes do have lower mutation rate than other microbes, with ciliated protozoa as extremely low cases; DNA mismatch repair is biased in repairing different types of mutations, etc.
  2. Applying mutation accumulation to antibiotic pharmacology. For this part, I am trying to answer: how low levels of antibiotics cause mutations and what kind of mutations are induced during antibiotics treatments in E. coli K-12 MG1655; whether mutator strains have higher chances of gaining resistance; are there any indications of oxidative mutations derived from antibiotic treatment? I am also expanding this kind of antibiotic induced mutations to pathogenic bacteria like Salmonella enterica, Staphylococcus aureus etc., as well as yeasts Saccharomyces cerevisiae, Candida albicans.

Selected Publications

Farlow, A.*, Long, H.*, Arnoux, S., Sung, W., Doak, T., Nordborg, M., Lynch, M. The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics (in press; * co-first-author).

Xu, S., Ackerman, M., Long, H., Bright, L., Spitze, K., Ramsdell, J.S., Thomas, W.K., Lynch, M. 2015. A male-specific genetic map of the microcrustacean Daphnia pulex based on single sperm whole-genome sequencing. Genetics 201(1):31-38.

Long, H.*, Kucukyildirim, S.*, Sung, W., Williams, E., Lee, H., Ackerman, M., Doak, T.G., Tang, H., Lynch, M. 2015. Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Molecular Biology and Evolution. 32(9): 2383-2392. (* co-first-author)

Long, H., Sung, W., Miller, S., Ackerman, M., Doak, T., Lynch, M. 2015. Mutation rate, spectrum, topology and context dependency in the DNA mismatch repair deficient Pseudomonas fluorescens. Genome Biology and Evolution 7(1): 262-271.

Long, H., Zufall, R. 2015. Mutational robustness of morphological traits in the ciliate Tetrahymena thermophila. Journal of Eukaryotic Microbiology 62(2): 249-254.

Long, H., Paixao, T., Azevedo, RBR, Zufall, RA. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics 195: 527-540

Long, H., Zufall, RA. 2010. Diverse modes of reproduction in the marine free-living ciliate Glauconema trihymene. BMC Microbiology. 10: 108. 

Long, H., Song, W., Al-Rasheid, K., Gong, J. 2009. Three marine haptorid ciliates from northern China: Paraspathidium apofuscum n. sp., Trachelotractus entzi (Kahl, 1927) Foissner, 1997 and Apotrachelotractus variabialis Long, Song & Warren, 2009. Journal of Natural History. 43: 1749-1761;

Long, H., Liu, H., Liu, W., et al. 2008. Two new ciliates from Hong Kong coastal water: Orthodonella sinica n. sp. and Apokeronopsis wrighti n. sp. (Protozoa: Ciliophora). Journal of Eukaryotic Microbiology. 55: 321-330;

Long, H., Song, W., Wang, Y. and Li, J. 2007. Morphological redescription of two endocommensal ciliates, Entorhipidium fukuii Uyemura, 1934 and Madsenia indomita (Madsen, 1931) Kahl, 1934 from digestive tracts of sea urchins of the Yellow Sea, China (Ciliophora; Scuticociliatida). European Journal of Protistology. 43: 101-114;

Long, H., Song, W., Warren, A., et al. 2007. Notes on two new marine ciliates from the north China seas, Schizocalyptra aeschtae nov. spec. and Sathrophilus holtae nov. spec., with new definition of the poorly-outlined genus Sathrophilus (Ciliophora, Oligohymenophora). Acta Protozoologica. 46: 229-245;

Long, H., Song, W., Chen, J., et al. 2006. Studies on an endoparasitic ciliate Boveria labialis (Protozoa: Ciliophora) from the sea cucumber, Apostichopus japonicus. Journal of Marine Biological Association, U. K. 86: 823-828.

Long, H., Song, W., Gong, J., et al. 2005. Frontonia lynni n. sp., a new marine ciliate (Protozoa, Ciliophora, Hymenostomatida) from Qingdao, China. Zootaxa 1003: 57-64.

Long, H. 2000. A useful solid geometry function. Mathematics and Physics World (High School Edition, in Chinese). 71: 42.